Mask in Wallace
Overview
Mask allows users to post-process the SDM you made in Wallace or imported with UserSDM. Users are given the option to mask using user-specified shapefiles, expert opinions, or remote sensing data. Additionally, Mask allows users to temporally match species occurrence records with remote sensing data (e.g., annual forest cover).
For more information about this component, please see our video: maskRangeR demonstration in Wallace.
Instructions
Thank you for testing our development version. Before you begin, please follow the Wallace v3 installation instructions and Download the prepared datasets.
Please find instructions for beta testing of the new functionalities within the Mask component below. You may choose to test all of these functionalities or either of them separately. You do not need to follow them sequentially though this is strongly recommended.
1. Running Wallace
- Open your R studio and run these lines of code in the console:
library(wallace)
run_wallace(biomodelos=TRUE) - Wallace should automatically open in your default browser (e.g., Google Chrome, Safari, Firefox).
2. Upload data & SDMs
Upload Occurrence data
Navigate to the Occ Data tab on the top menu bar.
Select the “User-specified” option on the side menu and upload the All_new_records_by_year.csv occurrence data file. These data will be used to test the Mask: temporal extract module.
- Note: When attempting to use the Temporal extract module with your own data, you must ensure that the occurrence .csv file provided includes a “year” column, with dates matching those of the MODIS data that you will upload in that module.
Upload an SDM
In addition to providing tools for users to build SDMs, Wallace now allows users to upload their own SDMs as raster files. To do so, navigate to the User SDM tab on the top menu.
Select Upload User SDM on the side menu and load the Bassaricyon_neblina.tif file that you downloaded - it is inside the olinguito.zip file.
Click Load SDM. This should upload a continuous model for Brassaricyon neblina, a small carnivore known as the Olinguito.
Note: All of the Mask modules can be executed using continuous model predictions. However, some ChangeRR functions (e.g., area calculations) will require a binary (thresholded) models.
If you also wish to test ChangeRR we suggest you use a thresholded model here instead. Make sure any model you upload in User SDM is projected and has the same name as the scientific name of your species occurrence csv file.
3. Test: Masking SDMs with shapefiles
Navigate to the Mask tab on the top menu.
Select Mask by Shapefile option in the sidebar and upload the SA_Ecoregions_WWF shapefile. This is WWF’s Terrestrial Ecoregions of the World.Note that you must upload all three files (.shp, .shx, .dbf).
INSERT IMAGE OF WHERE THE COMPONENT & MODULE ARE
Click “Load”.
You may see an error message- don’t worry, just click “OK”. Wallace is giving you a warning:
! WARNING:Bassaricyon neblina cloglog | Projection not found for shapefile. It is assume that shapefile datum is WGS84 (**) Scroll down to Step 2: Select Field: and select “ECO_NAME”.
First, deselect all names, and then select the 5 available options for “montane forest”.
NOTE: Blue sections will be removed, yellow will be kept.
Select Attribute:
- Cauca Valley montane forest
- Magdalena Valley montane forest
- Eastern Cordilla real montane forests
- Cordilla Oriental montane forest
- Northwestern Andean montane forests
Click “Mask”. This may take a few minutes.
You can then download your masked projection, continue masking, or move on to calculate indicators in ChangeRR.
4. Test: Masking SDMs using expert polygons
Navigate to the Mask tab in the top menu bar and select “Expert Polygon” in the side bar.
Scroll down to Step 1: Choose Input Polygon and select Draw Polygon from the drop-down menu.
Click on the polygon drawing tool on the map to create your own polygon. To close the polygon, make sure you click on the first vertex created.
Once you have created a polygon to your satisfaction, click the “Create” button.
Scroll down to Step 2: Choose action and select “Remove polygon”, then click the “Mask” button.
Note: When working with a continuous model prediction, you may only remove polygons. However, you can add or remove a polygon to a thresholded (binary) model prediction.
5. Test: Mask an SDM by temporally matching with remote sensing data
Navigate to the Mask tab in the top menu and then select “Temporal extract” in the side menu.
Scroll down to Step 1: Upload Temporal Rasters to upload environmental rasters for masking distribution: Select the 5 following MODIS Vegetation Continuous Fields (VCF) files:
2005_olinguito_Modis.tif
2006_olinguito_Modis.tif
2008_olinguito_Modis.tif
2009_olinguito_Modis.tif
2010_olinguito_Modis.tif
Click the “Load” button.
Scroll down to Step 2: Bounds to select the temporal time frame for which we will match our occurrence data.
Select only the years 2005, 2006, 2008, 2009, 2010. These are the years for which we have both MODIS VCF data and occurrence data.
Note Make sure you have previously uploaded the All_new_records_by_year.csv.
Click the “Get Bounds” button to get the distribution of MODIS VCF values corresponding to your occurrence points. These results can guide the selection of the upper and lower bounds for these values to create the SDM mask.
Scroll down to Step 3: Mask and select the 2010_olinguito_Modis.tif raster. This raster will be used to create a masking layer based on user-defined upper and lower MODIS VCF values.
Use the sliding bar to select upper and lower bounds for the MODIS VCF values you consider reasonable for the species. Note, that the Olinguito is strictly associated to cloud forests.
- Click “Mask” to remove areas from your SDM with MODIS VCF values that are not within the bounds of what is considered suitable for the Olinguito.
6. Download Mask
- To download the masked SDM, navigate to the “Download” tab in the results panel. Use the drop-down menu to select your preferred output file type and click on “Mask file” to download.
- If you want to continue testing ChangeRR, you can navigate to it on the top menu bar and follow testing instructions.